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Characterizing the genetic differences between two distinct migrant groups from Indo-European and Dravidian speaking populations in India.

Ali M, Liu X, Pillai EN, Chen P, Khor CC, Ong RT, Teo YY - BMC Genet. (2014)

Bottom Line: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India.These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH).Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Sciences Institute, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.

ABSTRACT

Background: India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Dravidian languages to Indo-European languages around 1500 B.C. is central to the Aryan Invasion Theory. Here we investigate the genetic differences between two sub-populations of India consisting of: (1) The Indo-European language speaking Gujarati Indians with genome-wide data from the International HapMap Project; and (2) the Dravidian language speaking Tamil Indians with genome-wide data from the Singapore Genome Variation Project.

Results: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India. These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). One of the regions that emerged spans the SLC24A5 gene that has been functionally shown to affect skin pigmentation, with a higher degree of genetic sharing between Gujarati Indians and Europeans.

Conclusions: Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

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Related in: MedlinePlus

Genetic differentiation between GIH and INS on chromosome 15. Evidence of genetic differentiation between GIH and INS on chromosome 15 between 45.5 Mb and 47.0 Mb from three discovery mechanisms that look for considerable regional differences in SNP allele frequencies (as quantified by the FST metric) relative to the genome (top panel); differential evidence of positive selection from iHS in GIH and INS (middle panel); XP-EHH signals contrasting GIH and INS that are found in either tails of the genome-wide distribution (bottom panel). In all three panels, SNPs exhibiting extreme evidence relative to the genome are displayed in differently in yellow, orange and red according to the respective percentiles as illustrated in the three figure legends. Genes located within this region are identified according to NCBI hg18 (build 36) coordinates.
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Figure 4: Genetic differentiation between GIH and INS on chromosome 15. Evidence of genetic differentiation between GIH and INS on chromosome 15 between 45.5 Mb and 47.0 Mb from three discovery mechanisms that look for considerable regional differences in SNP allele frequencies (as quantified by the FST metric) relative to the genome (top panel); differential evidence of positive selection from iHS in GIH and INS (middle panel); XP-EHH signals contrasting GIH and INS that are found in either tails of the genome-wide distribution (bottom panel). In all three panels, SNPs exhibiting extreme evidence relative to the genome are displayed in differently in yellow, orange and red according to the respective percentiles as illustrated in the three figure legends. Genes located within this region are identified according to NCBI hg18 (build 36) coordinates.

Mentions: A total of eight regions were identified from our analyses, of which six regions encompassed at least one gene (see Table 2). One of these six regions is the region on chromosome 15 between 45.7 Mb and 46.2 Mb, which encapsulated four genes including the solute carrier family 24 member 5 (SLC24A5) gene that has been associated with skin pigmentation[20] (Figure 4). This region was found to exhibit regional differences in allele frequencies at the top 0.1% of the genome-wide distribution, along with XP-EHH signals found at the extreme 0.1th percentile, where the direction of the XP-EHH region corresponded with evidence of positive selection in GIH relative to INS. A genome-wide association study of skin pigmentation in a South Asian population identified the guanine allele for the index SNP rs1834640 in SLC24A5 to be associated with lighter skin pigmentation, and this allele was present at a frequency of 4.7% in INS compared to 40.2% in GIH (FST = 18.1%), indicating that the differential evidence in this region concurs with the significant difference in the frequency of an allele that has been linked to skin pigmentation.


Characterizing the genetic differences between two distinct migrant groups from Indo-European and Dravidian speaking populations in India.

Ali M, Liu X, Pillai EN, Chen P, Khor CC, Ong RT, Teo YY - BMC Genet. (2014)

Genetic differentiation between GIH and INS on chromosome 15. Evidence of genetic differentiation between GIH and INS on chromosome 15 between 45.5 Mb and 47.0 Mb from three discovery mechanisms that look for considerable regional differences in SNP allele frequencies (as quantified by the FST metric) relative to the genome (top panel); differential evidence of positive selection from iHS in GIH and INS (middle panel); XP-EHH signals contrasting GIH and INS that are found in either tails of the genome-wide distribution (bottom panel). In all three panels, SNPs exhibiting extreme evidence relative to the genome are displayed in differently in yellow, orange and red according to the respective percentiles as illustrated in the three figure legends. Genes located within this region are identified according to NCBI hg18 (build 36) coordinates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4120727&req=5

Figure 4: Genetic differentiation between GIH and INS on chromosome 15. Evidence of genetic differentiation between GIH and INS on chromosome 15 between 45.5 Mb and 47.0 Mb from three discovery mechanisms that look for considerable regional differences in SNP allele frequencies (as quantified by the FST metric) relative to the genome (top panel); differential evidence of positive selection from iHS in GIH and INS (middle panel); XP-EHH signals contrasting GIH and INS that are found in either tails of the genome-wide distribution (bottom panel). In all three panels, SNPs exhibiting extreme evidence relative to the genome are displayed in differently in yellow, orange and red according to the respective percentiles as illustrated in the three figure legends. Genes located within this region are identified according to NCBI hg18 (build 36) coordinates.
Mentions: A total of eight regions were identified from our analyses, of which six regions encompassed at least one gene (see Table 2). One of these six regions is the region on chromosome 15 between 45.7 Mb and 46.2 Mb, which encapsulated four genes including the solute carrier family 24 member 5 (SLC24A5) gene that has been associated with skin pigmentation[20] (Figure 4). This region was found to exhibit regional differences in allele frequencies at the top 0.1% of the genome-wide distribution, along with XP-EHH signals found at the extreme 0.1th percentile, where the direction of the XP-EHH region corresponded with evidence of positive selection in GIH relative to INS. A genome-wide association study of skin pigmentation in a South Asian population identified the guanine allele for the index SNP rs1834640 in SLC24A5 to be associated with lighter skin pigmentation, and this allele was present at a frequency of 4.7% in INS compared to 40.2% in GIH (FST = 18.1%), indicating that the differential evidence in this region concurs with the significant difference in the frequency of an allele that has been linked to skin pigmentation.

Bottom Line: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India.These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH).Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Sciences Institute, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.

ABSTRACT

Background: India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Dravidian languages to Indo-European languages around 1500 B.C. is central to the Aryan Invasion Theory. Here we investigate the genetic differences between two sub-populations of India consisting of: (1) The Indo-European language speaking Gujarati Indians with genome-wide data from the International HapMap Project; and (2) the Dravidian language speaking Tamil Indians with genome-wide data from the Singapore Genome Variation Project.

Results: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India. These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). One of the regions that emerged spans the SLC24A5 gene that has been functionally shown to affect skin pigmentation, with a higher degree of genetic sharing between Gujarati Indians and Europeans.

Conclusions: Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

Show MeSH
Related in: MedlinePlus